If it died all the way back to the root stock, there is a good chance that the root stock is what is growing now and not your lemon tree. Root stock trees are typically used because they are hardy and they often produce little to no fruit that is inferior in quality anyway.

As the new growth look very different from the way it was, I think it is safe to say that your tree actually died and this is the root stock. I would recommend starting over with a new tree.